Package: spammR 0.99.26

Sara Gosline

spammR: SPatial Analysis of Multiomics Measurements in R

SpammR provides a suite of tools and a data structure to analyze diverse multiomics measurements in a spatial context. It enables the analysis and visualization of omics measurements paired with a specific image, each with spatial coordinates.

Authors:Sara Gosline [cre, aut], Harkirat Sohi [aut], Yannick Mahlich [aut]

spammR_0.99.26.tar.gz
spammR_0.99.26.zip(r-4.7-any)spammR_0.99.26.zip(r-4.6-any)spammR_0.99.26.zip(r-4.5-any)
spammR_0.99.26.tgz(r-4.6-any)spammR_0.99.26.tgz(r-4.5-any)
spammR_0.99.26.tar.gz(r-4.7-any)spammR_0.99.26.tar.gz(r-4.6-any)
spammR_0.99.26.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spammR/json (API)

# Install 'spammR' in R:
install.packages('spammR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pnnl-compbio/spammr/issues

Pkgdown/docs site:https://pnnl-compbio.github.io

Datasets:
  • oneKSoilsCoords - Soil sample coordinates for the sample information
  • oneKSoilsMeta - Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample information
  • pancMeta - Here is the data to be included in the spammR package
  • protMeta - Protein metadata for general uniprot data, including the pancProts column for the panc data
  • smallPancData - Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in 'pancMeta'. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962

On CRAN:

Conda:

spatialpathwaysproteomicsdifferentialexpressionmetabolomicssystemsbiologygeneexpressiongenesetenrichmentsoftwaretranscriptionsequencingmicroarrayepigeneticscheminformaticstranscriptomicscoveragenormalizationpreprocessingbayesianclusteringregressionexonarrayrnaseqonechanneltwochannelmicrornaarraymrnamicroarrayproprietaryplatformssinglecellcellbiologybiomedicalinformaticsfunctionalgenomicsimmunooncologyalternativesplicingdifferentialsplicingbatcheffectmultiplecomparisonqualitycontroltimecoursedataimportlipidomics

5.79 score 8 stars 13 exports 211 dependencies

Last updated from:6a00912bf8. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE236
linux-develNOTE458
source / vignettesOK457
linux-releaseNOTE442
macos-releaseNOTE332
macos-oldrelNOTE253
windows-develNOTE339
windows-releaseNOTE292
windows-oldrelNOTE307
wasm-releaseOK183

Exports:calc_missingnesscalc_spatial_diff_exconvert_to_spedistance_based_analysisenrich_gradientenrich_oraimpute_speretrieve_metaspace_dataspat_reducespatial_heatmapspatial_networksplit_spevolcano_plot

Dependencies:abindaskpassbackportsbase64encBiobaseBiocFileCacheBiocGenericsBiocManagerBiocStylebitbit64bitopsblobbookdownbootbroombslibcachemcallrcarcarDatacaToolscellrangerclassclassIntclicliprcolorspaceconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydplyrDTdtplyre1071evaluatefarverfastmapfilelockfontawesomeforcatsforecastFormulafracdifffsgarglegenericsGenomicRangesggforceggnewscaleggplot2ggpubrggraphggrepelggsciggsignifgluegoogledrivegooglesheets4gplotsgraphlayoutsgridExtragtablegtoolshavenherehighrhmshtmltoolshtmlwidgetshttrhttr2idsigraphimputeIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleapRlifecyclelimmalme4lmtestlubridatemagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigplotlypngpolyclippolynomprettyunitsprocessxprogresspromisesproxypspurrrquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLRdpackreadrreadxlreformulasrematchrematch2reprexreticulaterjsonrlangrmarkdownrprojrootRSQLiterstatixrstudioapirvests2S4ArraysS4VectorsS7sassscalesselectrSeqinfosfSingleCellExperimentspSparseArraySparseMSpatialExperimentspDataspdepstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsterratextshapingtibbletidygraphtidyrtidyselecttidyversetimechangetimeDatetinytextweenrtzdbunitsurcautf8uuidvctrsviridisviridisLitevroomwithrwkxfunxml2XVectoryamlzoo

spammR lipidomic and proteomic integration
About | Load proteomics data | Format data | Loading image coordinates rom GEOJson | Create SpatialExperiment Object | Load lipidomics data | Retrieve metaspace data | Add image data | Comparing Protein and Lipids | Merging images to single coordinate system | Correlation analysis | Looking for lipids associated with known proteins | Ascribing function to unknown lipids | Plot proteins | Summary | Session info
Rendered fromlipidProt.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2025-11-13

spammR microbiome evaluation
R and other dependencies | Metagenomic data formatting requirements | Geographic map formatting requirements | Mapping soil locations to map | get the "Pixel" x/y (NOT lat/long x/y) of metagenome samples | Exporting the rasterized map | Examplary plotting | Using spammR on metagenomic geographic data | Sample Metadata | CLEANING UP OF DATA | Create SpatialExperiment object | Metagenomic differential expression and enrichment | Spatial heatmap showing abundance of significant KO | Pathway enrichment | Session Information
Rendered fromspatMicrobiome.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2025-08-26

spammR Spatial Proteomics Example
Getting started | Collecting data to analyze | Data overview and examples | Omics Measurement Data | Sample metadata | Image files | Omics metadata | Loading data into spatial experiment object. | Spatial data with image | Expression and pathway analysis | Differential expression | Plot differentially expressed proteins | Pathway enrichment measurements | Pathway plotting | Distance based measurements | Plot protein gradient | Gradient-based enrichment | Plotting pathways from gradient | Network plotting | Summary | References | Session info
Rendered fromspatProt.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2025-03-18

Readme and manuals

Help Manual

Help pageTopics
Calculate centers of spots/samples for distance based analysiscalc_centers
Helper function for computing pairwise differences between sample valuescalc_diff_pairwiseSamples
Calculate degree of missingness for each featurea and samplecalc_missingness
Identify differentially abundant features across imagecalc_spatial_diff_ex
Create a 'SpatialExperiment' object from dataconvert_to_spe
Identify multiomic features correlated with an distance to an image featuredistance_based_analysis
Calculate functional or pathway enrichment from a gradientenrich_gradient
Calculate functional or pathway enrichmentenrich_ora
Impute missing values based on spatial coordinatesimpute_spe
Soil sample coordinates for the sample informationoneKSoilsCoords
Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample informationoneKSoilsMeta
Here is the data to be included in the spammR packagepancMeta
Protein metadata for general uniprot data, including the pancProts column for the panc dataprotMeta
Retrieve data objects from metaspaceretrieve_metaspace_data
Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in 'pancMeta'. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962smallPancData
Reduce a high resolution image measurement (origin) to a lower resolution measurement (target)spat_reduce
Plot data in heatmap together with imagespatial_heatmap
Plot network of correlated featuresspatial_network
Divide SPE object into smaller objects by column featuressplit_spe
Create a volcano plot from differential expression datavolcano_plot